import pathlib
from collections import Counter
import pandas as pd
import pyarrow.parquet as pq
from IPython.display import Image, display
from PIL import Image
import cytotable
# setup variables for use throughout the notebook
source_path = "/Users/eweisbar/Desktop/github/CytoTable/tests/data/cellprofiler/examplehuman"
dest_path = "/Users/eweisbar/Desktop/example.parquet"
list(pathlib.Path(source_path).glob("*"))
result = cytotable.convert(
source_path=source_path,
dest_path=dest_path,
# specify a destination data format type
dest_datatype="parquet",
# specify a preset which enables quick use of common input file formats
preset="cellprofiler_csv",
)
print(pathlib.Path(result).name)
pq.read_table(source=result).to_pandas().head()I created a new Python 3.11 conda environment.
I ran pip install cytotable and pip install ipykernel so I could run it from a Jupyter notebook.
---------------------------------------------------------------------------
BadStateException Traceback (most recent call last)
Cell In[2], [line 17](vscode-notebook-cell:?execution_count=2&line=17)
13 dest_path = "/Users/eweisbar/Desktop/example.parquet"
15 list(pathlib.Path(source_path).glob("*"))
---> [17](vscode-notebook-cell:?execution_count=2&line=17) result = cytotable.convert(
18 source_path=source_path,
19 dest_path=dest_path,
20 # specify a destination data format type
21 dest_datatype="parquet",
22 # specify a preset which enables quick use of common input file formats
23 preset="cellprofiler_csv",
24 )
25 print(pathlib.Path(result).name)
27 pq.read_table(source=result).to_pandas().head()
File ~/miniforge3/envs/cytotable/lib/python3.11/site-packages/cytotable/convert.py:1714, in convert(source_path, dest_path, dest_datatype, source_datatype, metadata, compartments, identifying_columns, concat, join, joins, chunk_size, infer_common_schema, drop_null, data_type_cast_map, add_tablenumber, page_keys, sort_output, preset, parsl_config, **kwargs)
1703 raise CytoTableException(
1704 (
1705 "When using join=True one must pass a 'join' pagination key "
(...) 1710 )
1711 )
1713 # send sources to be written to parquet if selected
-> [1714](https://file+.vscode-resource.vscode-cdn.net/Users/eweisbar/Desktop/github/CellProfiler-plugins/~/miniforge3/envs/cytotable/lib/python3.11/site-packages/cytotable/convert.py:1714) output = _run_export_workflow(
1715 source_path=source_path,
...
File "/Users/eweisbar/miniforge3/envs/cytotable/lib/python3.11/site-packages/parsl/executors/high_throughput/probe.py", line 67, in probe_addresses
raise ConnectionError(f"No viable ZMQ url from: {addys}")
ConnectionError: No viable ZMQ url from: tcp://73.42.154.156:54345, tcp://192.168.68.54:54345
I created a new Python 3.11 conda environment.
I ran
pip install cytotableandpip install ipykernelso I could run it from a Jupyter notebook.On first execution I got
ModuleNotFoundError: No module named 'PIL'so Ipip install Pillow.Now I'm getting
ConnectionError: No viable ZMQ url from: tcp://73.42.154.156:54345, tcp://192.168.68.54:54345whether I run it in Python or in my Jupyter notebook (though the tcp numbers vary).